Smiruthi Ramasubramanian wrote:
Justin,
I tried to use an index file with atom numbers of the water molecules in
the required volume.
But when I try to ionize the box, I get this error:
Fatal error:
The solvent group SOL is not continuous: index[717]=21689, index[718]=21696
This makes sense, but is there a way get around this?
The fundamental requirement of genion is that the solvent is continuous in the
coordinate file. If that's not true, genion won't work. If you have continuous
solvent, a valid index group within that section should work just fine.
-Justin
SR
On Thu, Mar 25, 2010 at 5:17 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Smiruthi Ramasubramanian wrote:
I am simulating an ion channel and require help placing a
concentration of ions at one side of the box (below the membrane).
"Sidedness" is irrelevant in a periodic system; the water layers are
continuous with PBC.
SETUP: membrane + embedded protein in the center of the cube.
I tried to generate a smaller cube (of the required volume below
the cube), solvate, add ions and then /cat/ with the *.gro file
of my system before solvating. But when I solvate the system
with ions, the ions are removed.
Any suggestions as to how to handle this problem?
I don't fully understand what you tried to do, but it should be
possible to solvate the unit cell normally, create an index group
for the waters on one "side" of the membrane, and pass this index
file to the -n flag of genion. Creating the index file may involve
writing your own script to collect the atom numbers. As far as I am
aware, make_ndx cannot, for example, select all water molecules
below/above some z-coordinate, which would be required for your
situation.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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